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Flores-Mireles D, Camacho-Villasana Y, Lutikurti M, García-Guerrero AE, Lozano-Rosas G, Chagoya V, Gutiérrez-Cirlos EB, Brandt U, Cabrera-Orefice A, Pérez-Martínez X. The cytochrome b carboxyl terminal region is necessary for mitochondrial complex III assembly. Life Sci Alliance 2023; 6:e202201858. [PMID: 37094942 PMCID: PMC10132202 DOI: 10.26508/lsa.202201858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
Mitochondrial bc 1 complex from yeast has 10 subunits, but only cytochrome b (Cytb) subunit is encoded in the mitochondrial genome. Cytb has eight transmembrane helices containing two hemes b for electron transfer. Cbp3 and Cbp6 assist Cytb synthesis, and together with Cbp4 induce Cytb hemylation. Subunits Qcr7/Qcr8 participate in the first steps of assembly, and lack of Qcr7 reduces Cytb synthesis through an assembly-feedback mechanism involving Cbp3/Cbp6. Because Qcr7 resides near the Cytb carboxyl region, we wondered whether this region is important for Cytb synthesis/assembly. Although deletion of the Cytb C-region did not abrogate Cytb synthesis, the assembly-feedback regulation was lost, so Cytb synthesis was normal even if Qcr7 was missing. Mutants lacking the Cytb C-terminus were non-respiratory because of the absence of fully assembled bc 1 complex. By performing complexome profiling, we showed the existence of aberrant early-stage subassemblies in the mutant. In this work, we demonstrate that the C-terminal region of Cytb is critical for regulation of Cytb synthesis and bc 1 complex assembly.
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Affiliation(s)
- Daniel Flores-Mireles
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Madhurya Lutikurti
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aldo E García-Guerrero
- Department of Medicine and Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Guadalupe Lozano-Rosas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Victoria Chagoya
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | | | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
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Rcf proteins and their differential specificity for respiratory chain complexes: A unique role for Rcf2 on oxygen sensitive supercomplexes? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119133. [PMID: 34450214 DOI: 10.1016/j.bbamcr.2021.119133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 11/22/2022]
Abstract
The respiratory chain, embedded in the inner mitochondrial membrane, is organized as a network of individual complexes, as well as large supercomplex structures. In the yeast S. cerevisiae, these supercomplexes consist of a dimeric cytochrome bc1-complex adjoined by one or two copies of cytochrome c oxidase. The formation of these complexes is a dynamic process and is regulated by various factors in order to adapt to environmental and metabolic changes. These adaptions occur at the level of enzyme regulation, complex assembly, as well as altered nuclear and mitochondrial transcription and translation. Members of the Rcf protein family (Rcf1, Rcf2 and Rcf3) are required for respiratory complex biogenesis and act mainly by regulating the assembly and enzyme activity of complex IV within supercomplexes. Rcf1 functions in the assembly process via the COX3 module, whereas Rcf2 and Rcf3 are responsible for enzymatic regulation. In this study, we have extended this knowledge to show that Rcf2 and Rcf3 can also associate with newly synthesized mitochondrial encoded proteins, such as Cox3, and therefore contribute to complex IV assembly. Since the Rcf proteins have overlapping regions of sequence similarities, we engineered novel fusion proteins of Rcf1 and Rcf3, with parts of Rcf2, to probe which of the Rcf protein domains can be attributed to their functions. The fusion proteins could compensate for the individual phenotypes of the complexIV assembly defect and the lack of complex IV regulation. Finally, the role of Rcf proteins for defined species of respiratory chain complexes in a hypoxic model was investigated, uncovering a unique association of Rcf2 with the hypoxic III2IV supercomplex. We therefore suggest an involvement of Rcf2 for adaption of the respiratory chain to altering oxygen levels.
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3
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Autophagy facilitates adaptation of budding yeast to respiratory growth by recycling serine for one-carbon metabolism. Nat Commun 2020; 11:5052. [PMID: 33028817 PMCID: PMC7542147 DOI: 10.1038/s41467-020-18805-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 09/08/2020] [Indexed: 01/07/2023] Open
Abstract
The mechanism and function of autophagy as a highly-conserved bulk degradation pathway are well studied, but the physiological role of autophagy remains poorly understood. We show that autophagy is involved in the adaptation of Saccharomyces cerevisiae to respiratory growth through its recycling of serine. On respiratory media, growth onset, mitochondrial initiator tRNA modification and mitochondrial protein expression are delayed in autophagy defective cells, suggesting that mitochondrial one-carbon metabolism is perturbed in these cells. The supplementation of serine, which is a key one-carbon metabolite, is able to restore mitochondrial protein expression and alleviate delayed respiratory growth. These results indicate that autophagy-derived serine feeds into mitochondrial one-carbon metabolism, supporting the initiation of mitochondrial protein synthesis and allowing rapid adaptation to respiratory growth. Autophagy is important during stress and development, but how the metabolites generated are used by the cell remains unclear. Here, the authors demonstrate that budding yeast require autophagy to provide serine for one-carbon metabolism during the switch from glycolytic to respiratory growth.
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Bruderek M, Jaworek W, Wilkening A, Rüb C, Cenini G, Förtsch A, Sylvester M, Voos W. IMiQ: a novel protein quality control compartment protecting mitochondrial functional integrity. Mol Biol Cell 2017; 29:256-269. [PMID: 29212875 PMCID: PMC5996957 DOI: 10.1091/mbc.e17-01-0027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 01/09/2023] Open
Abstract
Aggregation processes can cause severe perturbations of cellular homeostasis and are frequently associated with diseases. We performed a comprehensive analysis of mitochondrial quality and function in the presence of aggregation-prone polypeptides. Despite a significant aggregate formation inside mitochondria, we observed only a minor impairment of mitochondrial function. Detoxification of aggregated reporter polypeptides as well as misfolded endogenous proteins inside mitochondria takes place via their sequestration into a specific organellar deposit site we termed intramitochondrial protein quality control compartment (IMiQ). Only minor amounts of endogenous proteins coaggregated with IMiQ deposits and neither resolubilization nor degradation by the mitochondrial protein quality control system were observed. The single IMiQ aggregate deposit was not transferred to daughter cells during cell division. Detoxification of aggregates via IMiQ formation was highly dependent on a functional mitochondrial fission machinery. We conclude that the formation of an aggregate deposit is an important mechanism to maintain full functionality of mitochondria under proteotoxic stress conditions.
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Affiliation(s)
- Michael Bruderek
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Witold Jaworek
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Anne Wilkening
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Cornelia Rüb
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Giovanna Cenini
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Arion Förtsch
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Marc Sylvester
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Wolfgang Voos
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
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5
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García-Villegas R, Camacho-Villasana Y, Shingú-Vázquez MÁ, Cabrera-Orefice A, Uribe-Carvajal S, Fox TD, Pérez-Martínez X. The Cox1 C-terminal domain is a central regulator of cytochrome c oxidase biogenesis in yeast mitochondria. J Biol Chem 2017; 292:10912-10925. [PMID: 28490636 DOI: 10.1074/jbc.m116.773077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Cytochrome c oxidase (CcO) is the last electron acceptor in the respiratory chain. The CcO core is formed by mitochondrial DNA-encoded Cox1, Cox2, and Cox3 subunits. Cox1 synthesis is highly regulated; for example, if CcO assembly is blocked, Cox1 synthesis decreases. Mss51 activates translation of COX1 mRNA and interacts with Cox1 protein in high-molecular-weight complexes (COA complexes) to form the Cox1 intermediary assembly module. Thus, Mss51 coordinates both Cox1 synthesis and assembly. We previously reported that the last 15 residues of the Cox1 C terminus regulate Cox1 synthesis by modulating an interaction of Mss51 with Cox14, another component of the COA complexes. Here, using site-directed mutagenesis of the mitochondrial COX1 gene from Saccharomyces cerevisiae, we demonstrate that mutations P521A/P522A and V524E disrupt the regulatory role of the Cox1 C terminus. These mutations, as well as C terminus deletion (Cox1ΔC15), reduced binding of Mss51 and Cox14 to COA complexes. Mss51 was enriched in a translationally active form that maintains full Cox1 synthesis even if CcO assembly is blocked in these mutants. Moreover, Cox1ΔC15, but not Cox1-P521A/P522A and Cox1-V524E, promoted formation of aberrant supercomplexes in CcO assembly mutants lacking Cox2 or Cox4 subunits. The aberrant supercomplex formation depended on the presence of cytochrome b and Cox3, supporting the idea that supercomplex assembly factors associate with Cox3 and demonstrating that supercomplexes can be formed even if CcO is inactive and not fully assembled. Our results indicate that the Cox1 C-terminal end is a key regulator of CcO biogenesis and that it is important for supercomplex formation/stability.
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Affiliation(s)
- Rodolfo García-Villegas
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Yolanda Camacho-Villasana
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Miguel Ángel Shingú-Vázquez
- the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Alfredo Cabrera-Orefice
- the Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Salvador Uribe-Carvajal
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Thomas D Fox
- the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Xochitl Pérez-Martínez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico,
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6
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Ribosome-Associated Mba1 Escorts Cox2 from Insertion Machinery to Maturing Assembly Intermediates. Mol Cell Biol 2016; 36:2782-2793. [PMID: 27550809 PMCID: PMC5086520 DOI: 10.1128/mcb.00361-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/08/2016] [Accepted: 08/17/2016] [Indexed: 01/25/2023] Open
Abstract
The three conserved core subunits of the cytochrome c oxidase are encoded by mitochondria in close to all eukaryotes. The Cox2 subunit spans the inner membrane twice, exposing the N and C termini to the intermembrane space. For this, the N terminus is exported cotranslationally by Oxa1 and subsequently undergoes proteolytic maturation in Saccharomyces cerevisiae. Little is known about the translocation of the C terminus, but Cox18 has been identified to be a critical protein in this process. Here we find that the scaffold protein Cox20, which promotes processing of Cox2, is in complex with the ribosome receptor Mba1 and translating mitochondrial ribosomes in a Cox2-dependent manner. The Mba1-Cox20 complex accumulates when export of the C terminus of Cox2 is blocked by the loss of the Cox18 protein. While Cox20 engages with Cox18, Mba1 is no longer present at this stage. Our analyses indicate that Cox20 associates with nascent Cox2 and Mba1 to promote Cox2 maturation cotranslationally. We suggest that Mba1 stabilizes the Cox20-ribosome complex and supports the handover of Cox2 to the Cox18 tail export machinery.
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7
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Cooperation between COA6 and SCO2 in COX2 maturation during cytochrome c oxidase assembly links two mitochondrial cardiomyopathies. Cell Metab 2015; 21:823-33. [PMID: 25959673 DOI: 10.1016/j.cmet.2015.04.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/03/2015] [Accepted: 04/04/2015] [Indexed: 11/20/2022]
Abstract
Three mitochondria-encoded subunits form the catalytic core of cytochrome c oxidase, the terminal enzyme of the respiratory chain. COX1 and COX2 contain heme and copper redox centers, which are integrated during assembly of the enzyme. Defects in this process lead to an enzyme deficiency and manifest as mitochondrial disorders in humans. Here we demonstrate that COA6 is specifically required for COX2 biogenesis. Absence of COA6 leads to fast turnover of newly synthesized COX2 and a concomitant reduction in cytochrome c oxidase levels. COA6 interacts transiently with the copper-containing catalytic domain of newly synthesized COX2. Interestingly, similar to the copper metallochaperone SCO2, loss of COA6 causes cardiomyopathy in humans. We show that COA6 and SCO2 interact and that corresponding pathogenic mutations in each protein affect complex formation. Our analyses define COA6 as a constituent of the mitochondrial copper relay system, linking defects in COX2 metallation to cardiac cytochrome c oxidase deficiency.
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8
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Zamudio-Ochoa A, Camacho-Villasana Y, García-Guerrero AE, Pérez-Martínez X. The Pet309 pentatricopeptide repeat motifs mediate efficient binding to the mitochondrial COX1 transcript in yeast. RNA Biol 2014; 11:953-67. [PMID: 25181249 PMCID: PMC4179968 DOI: 10.4161/rna.29780] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial synthesis of Cox1, the largest subunit of the cytochrome c oxidase complex, is controlled by Mss51 and Pet309, two mRNA-specific translational activators that act via the COX1 mRNA 5′-UTR through an unknown mechanism. Pet309 belongs to the pentatricopeptide repeat (PPR) protein family, which is involved in RNA metabolism in mitochondria and chloroplasts, and its sequence predicts at least 12 PPR motifs in the central portion of the protein. Deletion of these motifs selectively disrupted translation but not accumulation of the COX1 mRNA. We used RNA coimmunoprecipitation assays to show that Pet309 interacts with the COX1 mRNA in vivo and that this association is present before processing of the COX1 mRNA from the ATP8/6 polycistronic mRNA. This association was not affected by deletion of 8 of the PPR motifs but was undetectable after deletion of the entire 12-PPR region. However, interaction of the Pet309 protein lacking 12 PPR motifs with the COX1 mRNA was detected after overexpression of the mutated form of the protein, suggesting that deletion of this region decreased the binding affinity for the COX1 mRNA without abolishing it entirely. Moreover, binding of Pet309 to the COX1 mRNA was affected by deletion of Mss51. This work demonstrates an in vivo physical interaction between a yeast mitochondrial translational activator and its target mRNA and shows the cooperativity of the PPR domains of Pet309 in interaction with the COX1 mRNA.
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Affiliation(s)
- Angélica Zamudio-Ochoa
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Aldo E García-Guerrero
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular; Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; México
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9
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Lytovchenko O, Naumenko N, Oeljeklaus S, Schmidt B, von der Malsburg K, Deckers M, Warscheid B, van der Laan M, Rehling P. The INA complex facilitates assembly of the peripheral stalk of the mitochondrial F1Fo-ATP synthase. EMBO J 2014; 33:1624-38. [PMID: 24942160 DOI: 10.15252/embj.201488076] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial F1Fo-ATP synthase generates the bulk of cellular ATP. This molecular machine assembles from nuclear- and mitochondria-encoded subunits. Whereas chaperones for formation of the matrix-exposed hexameric F1-ATPase core domain have been identified, insight into how the nuclear-encoded F1-domain assembles with the membrane-embedded Fo-region is lacking. Here we identified the INA complex (INAC) in the inner membrane of mitochondria as an assembly factor involved in this process. Ina22 and Ina17 are INAC constituents that physically associate with the F1-module and peripheral stalk, but not with the assembled F1Fo-ATP synthase. Our analyses show that loss of Ina22 and Ina17 specifically impairs formation of the peripheral stalk that connects the catalytic F1-module to the membrane embedded Fo-domain. We conclude that INAC represents a matrix-exposed inner membrane protein complex that facilitates peripheral stalk assembly and thus promotes a key step in the biogenesis of mitochondrial F1Fo-ATP synthase.
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Affiliation(s)
- Oleksandr Lytovchenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty for Biology, University of Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Bernhard Schmidt
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Karina von der Malsburg
- Institute for Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Freiburg, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty for Biology, University of Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Martin van der Laan
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany Institute for Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Bcs1p can rescue a large and productive cytochrome bc1 complex assembly intermediate in the inner membrane of yeast mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:91-101. [DOI: 10.1016/j.bbamcr.2010.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/15/2010] [Accepted: 08/11/2010] [Indexed: 11/23/2022]
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Mick DU, Vukotic M, Piechura H, Meyer HE, Warscheid B, Deckers M, Rehling P. Coa3 and Cox14 are essential for negative feedback regulation of COX1 translation in mitochondria. ACTA ACUST UNITED AC 2010; 191:141-54. [PMID: 20876281 PMCID: PMC2953447 DOI: 10.1083/jcb.201007026] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coa3 and Cox14 form assembly intermediates with newly synthesized Cox1 and are required for association of the Mss51 translational activator with these complexes. Regulation of eukaryotic cytochrome oxidase assembly occurs at the level of Cox1 translation, its central mitochondria-encoded subunit. Translation of COX1 messenger RNA is coupled to complex assembly in a negative feedback loop: the translational activator Mss51 is thought to be sequestered to assembly intermediates, rendering it incompetent to promote translation. In this study, we identify Coa3 (cytochrome oxidase assembly factor 3; Yjl062w-A), a novel regulator of mitochondrial COX1 translation and cytochrome oxidase assembly. We show that Coa3 and Cox14 form assembly intermediates with newly synthesized Cox1 and are required for Mss51 association with these complexes. Mss51 exists in equilibrium between a latent, translational resting, and a committed, translation-effective, state that are represented as distinct complexes. Coa3 and Cox14 promote formation of the latent state and thus down-regulate COX1 expression. Consequently, lack of Coa3 or Cox14 function traps Mss51 in the committed state and promotes Cox1 synthesis. Our data indicate that Coa1 binding to sequestered Mss51 in complex with Cox14, Coa3, and Cox1 is essential for full inactivation.
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Affiliation(s)
- David U Mick
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, D-79104 Freiburg, Germany
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12
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Shingú-Vázquez M, Camacho-Villasana Y, Sandoval-Romero L, Butler CA, Fox TD, Pérez-Martínez X. The carboxyl-terminal end of Cox1 is required for feedback assembly regulation of Cox1 synthesis in Saccharomyces cerevisiae mitochondria. J Biol Chem 2010; 285:34382-9. [PMID: 20807763 DOI: 10.1074/jbc.m110.161976] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synthesis of the largest cytochrome c oxidase (CcO) subunit, Cox1, on yeast mitochondrial ribosomes is coupled to assembly of CcO. The translational activator Mss51 is sequestered in early assembly intermediate complexes by an interaction with Cox14 that depends on the presence of newly synthesized Cox1. If CcO assembly is prevented, the level of Mss51 available for translational activation is reduced. We deleted the C-terminal 11 or 15 residues of Cox1 by site-directed mutagenesis of mtDNA. Although these deletions did not prevent respiratory growth of yeast, they eliminated the assembly-feedback control of Cox1 synthesis. Furthermore, these deletions reduced the strength of the Mss51-Cox14 interaction as detected by co-immunoprecipitation, confirming the importance of the Cox1 C-terminal residues for Mss51 sequestration. We surveyed a panel of mutations that block CcO assembly for the strength of their effect on Cox1 synthesis, both by pulse labeling and expression of the ARG8(m) reporter fused to COX1. Deletion of the nuclear gene encoding Cox6, one of the first subunits to be added to assembling CcO, caused the most severe reduction in Cox1 synthesis. Deletion of the C-terminal 15 amino acids of Cox1 increased Cox1 synthesis in the presence of each of these mutations, except pet54. Our data suggest a novel activity of Pet54 required for normal synthesis of Cox1 that is independent of the Cox1 C-terminal end.
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Affiliation(s)
- Miguel Shingú-Vázquez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF 04510, México
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13
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Merz S, Westermann B. Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae. Genome Biol 2009; 10:R95. [PMID: 19751518 PMCID: PMC2768984 DOI: 10.1186/gb-2009-10-9-r95] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/14/2009] [Indexed: 12/13/2022] Open
Abstract
A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis. Background The mitochondrial respiratory chain produces metabolic energy by oxidative phosphorylation. Biogenesis of the respiratory chain requires the coordinated expression of two genomes: the nuclear genome encoding the vast majority of mitochondrial proteins, and the mitochondrial genome encoding a handful of mitochondrial proteins. The understanding of the molecular processes contributing to respiratory chain assembly and maintenance requires the systematic identification and functional analysis of the genes involved. Results We pursued a systematic, genome-wide approach to define the sets of genes required for respiratory activity and maintenance and expression of the mitochondrial genome in yeast. By comparative gene deletion analysis we found an unexpected phenotypic plasticity among respiratory-deficient mutants, and we identified ten previously uncharacterized genes essential for respiratory growth (RRG1 through RRG10). Systematic functional analysis of 319 respiratory-deficient mutants revealed 16 genes essential for maintenance of the mitochondrial genome, 88 genes required for mitochondrial protein translation, and 10 genes required for expression of specific mitochondrial gene products. A group of mutants acquiring irreversible damage compromising respiratory capacity includes strains defective in assembly of the cytochrome c oxidase that were found to be particularly sensitive to aging. Conclusions These data advance the understanding of the molecular processes contributing to maintenance of the mitochondrial genome, mitochondrial protein translation, and assembly of the respiratory chain. They revealed a number of previously uncharacterized components, and provide a comprehensive picture of the molecular processes required for respiratory activity in a simple eukaryotic cell.
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Affiliation(s)
- Sandra Merz
- Institut für Zellbiologie, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany.
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14
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Perez-Martinez X, Butler CA, Shingu-Vazquez M, Fox TD. Dual functions of Mss51 couple synthesis of Cox1 to assembly of cytochrome c oxidase in Saccharomyces cerevisiae mitochondria. Mol Biol Cell 2009; 20:4371-80. [PMID: 19710419 DOI: 10.1091/mbc.e09-06-0522] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Functional interactions of the translational activator Mss51 with both the mitochondrially encoded COX1 mRNA 5'-untranslated region and with newly synthesized unassembled Cox1 protein suggest that it has a key role in coupling Cox1 synthesis with assembly of cytochrome c oxidase. Mss51 is present at levels that are near rate limiting for expression of a reporter gene inserted at COX1 in mitochondrial DNA, and a substantial fraction of Mss51 is associated with Cox1 protein in assembly intermediates. Thus, sequestration of Mss51 in assembly intermediates could limit Cox1 synthesis in wild type, and account for the reduced Cox1 synthesis caused by most yeast mutations that block assembly. Mss51 does not stably interact with newly synthesized Cox1 in a mutant lacking Cox14, suggesting that the failure of nuclear cox14 mutants to decrease Cox1 synthesis, despite their inability to assemble cytochrome c oxidase, is due to a failure to sequester Mss51. The physical interaction between Mss51 and Cox14 is dependent upon Cox1 synthesis, indicating dynamic assembly of early cytochrome c oxidase intermediates nucleated by Cox1. Regulation of COX1 mRNA translation by Mss51 seems to be an example of a homeostatic mechanism in which a positive effector of gene expression interacts with the product it regulates in a posttranslational assembly process.
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Affiliation(s)
- Xochitl Perez-Martinez
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F. 04510, México
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Kucejova B, Li L, Wang X, Giannattasio S, Chen XJ. Pleiotropic effects of the yeast Sal1 and Aac2 carriers on mitochondrial function via an activity distinct from adenine nucleotide transport. Mol Genet Genomics 2008; 280:25-39. [PMID: 18431598 PMCID: PMC2749980 DOI: 10.1007/s00438-008-0342-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 04/03/2008] [Indexed: 11/25/2022]
Abstract
In Saccharomyces cerevisiae, SAL1 encodes a Ca2+ -binding mitochondrial carrier. Disruption of SAL1 is synthetically lethal with the loss of a specific function associated with the Aac2 isoform of the ATP/ADP translocase. This novel activity of Aac2 is defined as the V function (for Viability of aac2 sal1 double mutant), which is independent of the ATP/ADP exchange activity required for respiratory growth (the R function). We found that co-inactivation of SAL1 and AAC2 leads to defects in mitochondrial translation and mitochondrial DNA (mtDNA) maintenance. Additionally, sal1Delta exacerbates the respiratory deficiency and mtDNA instability of ggc1Delta, shy1Delta and mtg1Delta mutants, which are known to reduce mitochondrial protein synthesis or protein complex assembly. The V function is complemented by the human Short Ca2+ -binding Mitochondrial Carrier (SCaMC) protein, SCaMC-2, a putative ATP-Mg/Pi exchangers on the inner membrane. However, mitochondria lacking both Sal1p and Aac2p are not depleted of adenine nucleotides. The Aac2R252I and Aac2R253I variants mutated at the R252-254 triplet critical for nucleotide transport retain the V function. Likewise, Sal1p remains functionally active when the R479I and R481I mutations were introduced into the structurally equivalent R479-T480-R481 motif. Finally, we found that the naturally occurring V-R+ Aac1 isoform of adenine nucleotide translocase partially gains the V function at the expense of the R function by introducing the mutations P89L and A96 V. Thus, our data support the view that the V function is independent of adenine nucleotide transport associated with Sal1p and Aac2p and this evolutionarily conserved activity affects multiple processes in mitochondria.
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Affiliation(s)
- Blanka Kucejova
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148,USA
| | - Li Li
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148,USA
| | - Xiaowen Wang
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148,USA
| | | | - Xin Jie Chen
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148,USA
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16
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Bauerschmitt H, Funes S, Herrmann JM. Synthesis and sorting of mitochondrial translation products. Methods Mol Biol 2008; 457:95-112. [PMID: 19066021 DOI: 10.1007/978-1-59745-261-8_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mitochondria are essential organelles of eukaryotic cells. The biogenesis of mitochondria depends on the coordinated function of two separate genetic systems: one in the nucleus and one in the organelle. The study of mitochondria requires the analysis of both genetic systems and their protein products. In this chapter, we focus on the translation and sorting of mitochondrially encoded proteins into the mitochondrial inner membrane in the baker's yeast Saccharomyces cerevisiae. The starting point is the labeling of these proteins, followed by some of the methods developed to investigate their topology and membrane incorporation. The methods described here can be applied also to the study of other aspects of organelle biogenesis such as folding, assembly, and degradation of proteins.
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Affiliation(s)
- Heike Bauerschmitt
- Adolf-Butenandt-Institute of Physiological Chemistry, University of Munich, Munich, Germany
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17
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Tavares-Carreón F, Camacho-Villasana Y, Zamudio-Ochoa A, Shingú-Vázquez M, Torres-Larios A, Pérez-Martínez X. The pentatricopeptide repeats present in Pet309 are necessary for translation but not for stability of the mitochondrial COX1 mRNA in yeast. J Biol Chem 2007; 283:1472-1479. [PMID: 18039654 DOI: 10.1074/jbc.m708437200] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pet309 is a protein essential for respiratory growth. It is involved in translation of the yeast mitochondrial COX1 gene, which encodes subunit I of the cytochrome c oxidase. Pet309 is also involved in stabilization of the COX1 mRNA. Mutations in a similar human protein, Lrp130, are associated with Leigh syndrome, where cytochrome c oxidase activity is affected. The sequence of Pet309 reveals the presence of at least seven pentatricopeptide repeats (PPRs) located in tandem in the central portion of the protein. Proteins containing PPR motifs are present in mitochondria and chloroplasts and are in general involved in RNA metabolism. Despite the increasing number of proteins from this family found to play essential roles in mitochondria and chloroplasts, little is understood about the mechanism of action of the PPR domains present in these proteins. In a series of in vivo analyses we constructed a pet309 mutant lacking the PPR motifs. Although the stability of the COX1 mRNA was not affected, synthesis of Cox1 was abolished. The deletion of one PPR motif at a time showed that all the PPR motifs are required for COX1 mRNA translation and respiratory growth. Mutations of basic residues in PPR3 caused reduced respiratory growth. According to a molecular model, these residues are facing a central cavity that could be involved in mRNA-binding activity, forming a possible path for this molecule on Pet309. Our results show that the RNA metabolism function of Pet309 is found in at least two separate domains of the protein.
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Affiliation(s)
- Faviola Tavares-Carreón
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, Mexico
| | - Yolanda Camacho-Villasana
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, Mexico
| | - Angélica Zamudio-Ochoa
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, Mexico
| | - Miguel Shingú-Vázquez
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, Mexico
| | - Alfredo Torres-Larios
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, Mexico
| | - Xochitl Pérez-Martínez
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, Mexico.
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18
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Mick DU, Wagner K, van der Laan M, Frazier AE, Perschil I, Pawlas M, Meyer HE, Warscheid B, Rehling P. Shy1 couples Cox1 translational regulation to cytochrome c oxidase assembly. EMBO J 2007; 26:4347-58. [PMID: 17882259 PMCID: PMC2034671 DOI: 10.1038/sj.emboj.7601862] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 08/24/2007] [Indexed: 11/09/2022] Open
Abstract
Cytochrome c oxidase (complex IV) of the respiratory chain is assembled from nuclear and mitochondrially-encoded subunits. Defects in the assembly process lead to severe human disorders such as Leigh syndrome. Shy1 is an assembly factor for complex IV in Saccharomyces cerevisiae and mutations of its human homolog, SURF1, are the most frequent cause for Leigh syndrome. We report that Shy1 promotes complex IV biogenesis through association with different protein modules; Shy1 interacts with Mss51 and Cox14, translational regulators of Cox1. Additionally, Shy1 associates with the subcomplexes of complex IV that are potential assembly intermediates. Formation of these subcomplexes depends on Coa1 (YIL157c), a novel assembly factor that cooperates with Shy1. Moreover, partially assembled forms of complex IV bound to Shy1 and Cox14 can associate with the bc1 complex to form transitional supercomplexes. We suggest that Shy1 links Cox1 translational regulation to complex IV assembly and supercomplex formation.
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Affiliation(s)
- David U Mick
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Freiburg, Germany
- Fakultät für Biologie, Universität Freiburg, Freiburg, Germany
| | - Karina Wagner
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Freiburg, Germany
- Fakultät für Biologie, Universität Freiburg, Freiburg, Germany
| | - Martin van der Laan
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Freiburg, Germany
| | - Ann E Frazier
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Freiburg, Germany
- Department of Biochemistry, La Trobe University, Melbourne, Australia
| | - Inge Perschil
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Freiburg, Germany
| | - Magdalena Pawlas
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Helmut E Meyer
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Bettina Warscheid
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Peter Rehling
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Freiburg, Germany
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, Hermann-Herder-Straße 7, Freiburg 79104, Germany. Tel.: +49 761 203 5245; Fax: +49 761 203 5245; E-mail:
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19
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Pierrel F, Bestwick ML, Cobine PA, Khalimonchuk O, Cricco JA, Winge DR. Coa1 links the Mss51 post-translational function to Cox1 cofactor insertion in cytochrome c oxidase assembly. EMBO J 2007; 26:4335-46. [PMID: 17882260 PMCID: PMC2034670 DOI: 10.1038/sj.emboj.7601861] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 08/09/2007] [Indexed: 11/08/2022] Open
Abstract
The assembly of cytochrome c oxidase (CcO) in yeast mitochondria is shown to be dependent on a new assembly factor designated Coa1 that associates with the mitochondrial inner membrane. Translation of the mitochondrial-encoded subunits of CcO occurs normally in coa1Delta cells, but these subunits fail to accumulate. The respiratory defect in coa1Delta cells is suppressed by high-copy MSS51, MDJ1 and COX10. Mss51 functions in Cox1 translation and elongation, whereas Cox10 participates in the biosynthesis of heme a, a key cofactor of CcO. Respiration in coa1Delta and shy1Delta cells is enhanced when Mss51 and Cox10 are coexpressed. Shy1 has been implicated in formation of the heme a3-Cu(B) site in Cox1. The interaction between Coa1 and Cox1, and the physical and genetic interactions between Coa1 and Mss51, Shy1 and Cox14 suggest that Coa1 coordinates the transition of newly synthesized Cox1 from the Mss51:Cox14 complex to the heme a cofactor insertion involving Shy1. coa1Delta cells also display a mitochondrial copper defect suggesting that Coa1 may have a direct link to copper metallation of CcO.
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Affiliation(s)
- Fabien Pierrel
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, Salt Lake City, UT, USA
| | - Megan L Bestwick
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, Salt Lake City, UT, USA
| | - Paul A Cobine
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, Salt Lake City, UT, USA
| | - Oleh Khalimonchuk
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, Salt Lake City, UT, USA
| | - Julia A Cricco
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, Salt Lake City, UT, USA
| | - Dennis R Winge
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, Salt Lake City, UT, USA
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, University of Utah, 50 North 1900 East, Salt Lake City, UT 84132, USA. Tel.: +1 801 585 5103; Fax: +1 801 585 5469; E-mail:
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20
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Nowikovsky K, Reipert S, Devenish RJ, Schweyen RJ. Mdm38 protein depletion causes loss of mitochondrial K+/H+ exchange activity, osmotic swelling and mitophagy. Cell Death Differ 2007; 14:1647-56. [PMID: 17541427 DOI: 10.1038/sj.cdd.4402167] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Loss of the MDM38 gene product in yeast mitochondria results in a variety of phenotypic effects including reduced content of respiratory chain complexes, altered mitochondrial morphology and loss of mitochondrial K(+)/H(+) exchange activity resulting in osmotic swelling. By use of doxycycline-regulated shut-off of MDM38 gene expression, we show here that loss of K(+)/H(+) exchange activity and mitochondrial swelling are early events, associated with a reduction in membrane potential and fragmentation of the mitochondrial reticulum. Changes in the pattern of mitochondrially encoded proteins are likely to be secondary to the loss of K(+)/H(+) exchange activity. The use of a novel fluorescent biosensor directed to the mitochondrial matrix revealed that the loss of K(+)/H(+) exchange activity was immediately followed by morphological changes of mitochondria and vacuoles, the close association of these organelles and finally uptake of mitochondrial material by vacuoles. Nigericin, a K(+)/H(+) ionophore, fully prevented these effects of Mdm38p depletion. We conclude that osmotic swelling of mitochondria triggers selective mitochondrial autophagy or mitophagy.
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Affiliation(s)
- K Nowikovsky
- Department of Genetics, Max F Perutz Laboratories, University of Vienna, Vienna, Austria
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21
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Fiumera HL, Broadley SA, Fox TD. Translocation of mitochondrially synthesized Cox2 domains from the matrix to the intermembrane space. Mol Cell Biol 2007; 27:4664-73. [PMID: 17452441 PMCID: PMC1951498 DOI: 10.1128/mcb.01955-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The N-terminal and C-terminal domains of mitochondrially synthesized cytochrome c oxidase subunit II, Cox2, are translocated through the inner membrane to the intermembrane space (IMS). We investigated the distinct mechanisms of N-tail and C-tail export by analysis of epitope-tagged Cox2 variants encoded in Saccharomyces cerevisiae mitochondrial DNA. Both the N and C termini of a truncated protein lacking the Cox2 C-terminal domain were translocated to the IMS via a pathway dependent upon the conserved translocase Oxa1. The topology of this Cox2 variant, accumulated at steady state, was largely but not completely unaffected in mutants lacking proteins required for export of the C-tail domain, Cox18 and Mss2. C-tail export was blocked by truncation of the last 40 residues from the C-tail domain, indicating that sequence and/or structural features of this domain are required for its translocation. Mss2, a peripheral protein bound to the inner surface of the inner membrane, coimmunoprecipitated with full-length newly synthesized Cox2, whose leader peptide had already been cleaved in the IMS. Our data suggest that the C-tail domain is recognized posttranslationally by a specialized translocation apparatus after the N-tail has been translocated by Oxa1.
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Affiliation(s)
- Heather L Fiumera
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853-2703, USA
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22
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19 Analysis of Gene Function of Mitochondria. J Microbiol Methods 2007. [DOI: 10.1016/s0580-9517(06)36019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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23
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Abstract
Mitochondrial biogenesis is an intricate process that requires the coordinated function of two separate genetic systems: one in the organelle and one in the nucleus. The study of mitochondria requires the analysis of both genetic systems and their protein products. We describe the general procedures used to label mitochondrially encoded proteins in the baker's yeast Saccharomyces cerevisiae, a starting point for the investigation of various aspects of organelle biogenesis, such as folding and assembly, sorting, and degradation of proteins.
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Affiliation(s)
- Soledad Funes
- Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München, Germany
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24
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Frazier AE, Taylor RD, Mick DU, Warscheid B, Stoepel N, Meyer HE, Ryan MT, Guiard B, Rehling P. Mdm38 interacts with ribosomes and is a component of the mitochondrial protein export machinery. ACTA ACUST UNITED AC 2006; 172:553-64. [PMID: 16476776 PMCID: PMC2063675 DOI: 10.1083/jcb.200505060] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Saccharomyces cerevisiae Mdm38 and Ylh47 are homologues of human Letm1, a protein implicated in Wolf-Hirschhorn syndrome. We analyzed the function of Mdm38 and Ylh47 in yeast mitochondria to gain insight into the role of Letm1. We find that mdm38Δ mitochondria have reduced amounts of certain mitochondrially encoded proteins and low levels of complex III and IV and accumulate unassembled Atp6 of complex V of the respiratory chain. Mdm38 is especially required for efficient transport of Atp6 and cytochrome b across the inner membrane, whereas Ylh47 plays a minor role in this process. Both Mdm38 and Ylh47 form stable complexes with mitochondrial ribosomes, similar to what has been reported for Oxa1, a central component of the mitochondrial export machinery. Our results indicate that Mdm38 functions as a component of an Oxa1-independent insertion machinery in the inner membrane and that Mdm38 plays a critical role in the biogenesis of the respiratory chain by coupling ribosome function to protein transport across the inner membrane.
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Affiliation(s)
- Ann E Frazier
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany
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25
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Preuss M, Ott M, Funes S, Luirink J, Herrmann JM. Evolution of mitochondrial oxa proteins from bacterial YidC. Inherited and acquired functions of a conserved protein insertion machinery. J Biol Chem 2005; 280:13004-11. [PMID: 15654078 DOI: 10.1074/jbc.m414093200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the Oxa1/YidC family are involved in the biogenesis of membrane proteins. In bacteria, YidC catalyzes the insertion and assembly of proteins of the inner membrane. Mitochondria of animals, fungi, and plants harbor two distant homologues of YidC, Oxa1 and Cox18/Oxa2. Oxa1 plays a pivotal role in the integration of mitochondrial translation products into the inner membrane of mitochondria. It contains a C-terminal ribosome-binding domain that physically interacts with mitochondrial ribosomes to facilitate the co-translational insertion of nascent membrane proteins. The molecular function of Cox18/Oxa2 is not well understood. Employing a functional complementation approach with mitochondria-targeted versions of YidC we show that YidC is able to functionally replace both Oxa1 and Cox18/Oxa2. However, to integrate mitochondrial translation products into the inner membrane of mitochondria, the ribosome-binding domain of Oxa1 has to be appended onto YidC. On the contrary, the fusion of the ribosome-binding domain onto YidC prevents its ability to complement COX18 mutants suggesting an indispensable post-translational activity of Cox18/Oxa2. Our observations suggest that during evolution of mitochondria from their bacterial ancestors the two descendents of YidC functionally segregated to perform two distinct activities, one co-translational and one post-translational.
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Affiliation(s)
- Marc Preuss
- Institut für Physiologische Chemie, Universität München, Butenandtstrasse 5, 81377 München, Germany
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26
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Tzagoloff A, Barrientos A, Neupert W, Herrmann JM. Atp10p assists assembly of Atp6p into the F0 unit of the yeast mitochondrial ATPase. J Biol Chem 2004; 279:19775-80. [PMID: 14998992 DOI: 10.1074/jbc.m401506200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The F(0)F(1)-ATPase complex of yeast mitochondria contains three mitochondrial and at least 17 nuclear gene products. The coordinate assembly of mitochondrial and cytosolic translation products relies on chaperones and specific factors that stabilize the pools of some unassembled subunits. Atp10p was identified as a mitochondrial inner membrane component necessary for the biogenesis of the hydrophobic F(0) sector of the ATPase. Here we show that, following its synthesis on mitochondrial ribosomes, subunit 6 of the ATPase (Atp6p) can be cross-linked to Atp10p. This interaction is required for the integration of Atp6p into a partially assembled subcomplex of the ATPase. Pulse labeling and chase of mitochondrial translation products in vivo indicate that Atp6p is less stable and more rapidly degraded in an atp10 null mutant than in wild type. Based on these observations, we propose Atp10p to be an Atp6p-specific chaperone that facilitates the incorporation of Atp6p into an intermediate subcomplex of ATPase subunits.
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Affiliation(s)
- Alexander Tzagoloff
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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27
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Szyrach G, Ott M, Bonnefoy N, Neupert W, Herrmann JM. Ribosome binding to the Oxa1 complex facilitates co-translational protein insertion in mitochondria. EMBO J 2004; 22:6448-57. [PMID: 14657018 PMCID: PMC291818 DOI: 10.1093/emboj/cdg623] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Oxa1 translocase of the mitochondrial inner membrane facilitates the insertion of both mitochondrially and nuclear-encoded proteins from the matrix into the inner membrane. Most mitochondrially encoded proteins are hydrophobic membrane proteins which are integrated into the lipid bilayer during their synthesis on mitochondrial ribosomes. The molecular mechanism of this co-translational insertion process is unknown. Here we show that the matrix-exposed C-terminus of Oxa1 forms an alpha-helical domain that has the ability to bind to mitochondrial ribosomes. Deletion of this Oxa1 domain strongly diminished the efficiency of membrane insertion of subunit 2 of cytochrome oxidase, a mitochondrially encoded substrate of the Oxa1 translocase. This suggests that co-translational membrane insertion of mitochondrial translation products is facilitated by a physical interaction of translation complexes with the membrane-bound translocase.
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Affiliation(s)
- Gregor Szyrach
- Institut für Physiologische Chemie, Butenandtstrasse 5, D-81377 München, Germany
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28
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Funes S, Nargang FE, Neupert W, Herrmann JM. The Oxa2 protein of Neurospora crassa plays a critical role in the biogenesis of cytochrome oxidase and defines a ubiquitous subbranch of the Oxa1/YidC/Alb3 protein family. Mol Biol Cell 2004; 15:1853-61. [PMID: 14767059 PMCID: PMC379281 DOI: 10.1091/mbc.e03-11-0789] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Proteins of the Oxa1/YidC/Alb3 family mediate the insertion of proteins into membranes of mitochondria, bacteria, and chloroplasts. Here we report the identification of a second gene of the Oxa1/YidC/Alb3 family in the genome of Neurospora crassa, which we have named oxa2. Its gene product, Oxa2, is located in the inner membrane of mitochondria. Deletion of the oxa2 gene caused a specific defect in the biogenesis of cytochrome oxidase and resulted in induction of the alternative oxidase (AOD), which bypasses the need for complex IV of the respiratory chain. The Oxa2 protein of N. crassa complements Cox18-deficient yeast mutants suggesting a common function for both proteins. The oxa2 sequence allowed the identification of a new subfamily of Oxa1/YidC/Alb3 proteins whose members appear to be ubiquitously present in mitochondria of fungi, plants, and animals including humans.
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Affiliation(s)
- Soledad Funes
- Institut für Physiologische Chemie, Universität München, 81377 München, Germany
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29
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Abstract
The biogenesis of mitochondria requires the insertion of both nuclear and mitochondrially encoded proteins into the inner membrane. The inner membrane protein Oxa1 plays an important role in this process. Translocation of the terminal intermembrane space domains of subunit 2 of the cytochrome oxidase complex, Cox2, strictly depends on Oxa1. In contrast, other Oxa1 substrates can be inserted independently of Oxa1 function, although at reduced efficiency. A Saccharomyces cerevisiae mutant containing a large deletion in its mitochondrial genome allowed us to analyze the insertion process of a fusion protein of cytochrome b and Cox2. In this mutant, the N-terminal domain of Cox2 is synthesized as a hairpin loop that is flanked by hydrophobic transmembrane segments on both sides. Both genetic and biochemical evidences indicate that translocation of this region across the inner membrane still requires Oxa1 function. Thus, the position of intermembrane space domains within protein sequences does not appear to determine their dependence on the Oxa1 translocase. Our observations rather suggest that the dependence on Oxa1 correlates with the net charge of the domain that has to be translocated across the lipid bilayer.
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Affiliation(s)
- Johannes M Herrmann
- Institut für Physiologische Chemie, Universität München, Butenandtstrasse 5, München 81377, Germany.
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30
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Perez-Martinez X, Broadley SA, Fox TD. Mss51p promotes mitochondrial Cox1p synthesis and interacts with newly synthesized Cox1p. EMBO J 2003; 22:5951-61. [PMID: 14592991 PMCID: PMC275423 DOI: 10.1093/emboj/cdg566] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The post-transcriptional role of Mss51p in mitochondrial gene expression is of great interest since MSS51 mutations suppress the respiratory defect caused by shy1 mutations. SHY1 is a Saccharomyces cerevisiae homolog of human SURF1, which when mutated causes a cytochrome oxidase assembly defect. We found that MSS51 is required for expression of the mitochondrial reporter gene ARG8(m) when it is inserted at the COX1 locus, but not when it is at COX2 or COX3. Unlike the COX1 mRNA-specific translational activator PET309, MSS51 has at least two targets in COX1 mRNA. MSS51 acts in the untranslated regions of the COX1 mRNA, since it was required to synthesize Arg8p when ARG8(m) completely replaced the COX1 codons. MSS51 also acts on a target specified by the COX1 coding region, since it was required to translate either COX1 or COX1:: ARG8(m) coding sequences from an ectopic COX2 locus. Mss51p was found to interact physically with newly synthesized Cox1p, suggesting that it could coordinate Cox1p synthesis with insertion into the inner membrane or cytochrome oxidase assembly.
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Affiliation(s)
- Xochitl Perez-Martinez
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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